MCDS software was developed by Dr Zhenyu Shi. It has powerful functions for plasmid design and management. It is free.
Reference: Shi, Zhenyu and Vickers, Claudia E.
(2016) Molecular Cloning Designer Simulator (MCDS):
all-in-one molecular cloning and genetic engineering design,
simulation and management software for complex synthetic
biology and metabolic engineering projects. Metabolic
Engineering Communications, 3 173-186.